The Darkest Shadows
by DarkPlague689
Summary: It took many years to do what he planned, and now it is nearly complete. All he has to do is establish himself as part of the league, steal some Pokémon. Then go to the final step. The Pokémon world will never be the same. Most certainly when he is through with it. (I do not own Pokémon.) poll is up.
1. Chapter 1(Rewritten)

The Orre Region, the wasteland of the Pokémon world. Nothing more than a big ass volcano surrounded by desserts. Well that is what it was before I came along. I sat in my office at the top of Mt. Battle overlooking the thriving green landscape of my region. Yes, I turned the wasteland into a beautiful paradise thanks to the help of two titan Pokémon, and by titan Pokémon I mean Kyogre and Groudon. Who would have ever thought that the worst of enemies could come together if their respective orbs were wielded by the same individuals? Archie and Maxie, were not the sharpest tool in the shed, but I digress.

I could feel myself smirk as I thought more about the events that were to unfold. It had taken me a few years to locate The Orre Region, a year to train my Pokémon to peak condition, a few more to locate and secure the Kyogre and Groudon, and a year to successfully terraform the Orre region and be named a hero. That however was just beginning. I had built gyms and a massive stadium all for the sake of hosting a massive tournament of sorts, only so that I could be steal the best trainers Pokémon, and use them to help me obtain three of the strongest Pokémon in existence. Cyrus wasn't entirely wrong on what he was doing, he just didn't have the means to do so, nor did he truly understand human nature. We humans live to fulfill our own selfish desires no matter the cost. I would use the power of the higher b beings to bring peace to this world, by eliminating human nature. Then the human race and even the Pokémon would be saved.

I Continue to stare at the at the Orre region landscape before I made my way to the far side of my office where a bookshelf resided. I gently pulled out the book 'Pokémon for beginners', underneath it was a little red button. I pressed the said button and the bookshelf began to shift. In a few seconds the bookshelf moved to its left revealing an elevator. I entered the said elevator, and was greeted by Delilah.

"How are you today, sir?" Delilah asked. Delilah was an artificial intelligence, I had created in memory of my mother. She listens only to me, and runs things while I am away, notifying me if anything occurs.

"I am good. Take me to sublevel D?" I asked.

"Going to see the prisoner today, sir?" Delilah asked.

"Yes." I replied. Subfloors where named after letters instead of negative integers, so there was no confusion with the staff. However, Sublevel D was only a level I could access. It housed, a very important prisoner. You see my methods of capturing other trainers' Pokémon, is very similar to what Team Snagem had done, however instead of a big bulky contraptions my gym leaders and elite four utilize special rings. The only problem was that the Pokémon could be recaptured. Wes, former member of team Snaggem, was still in the orre region somewhere. He was the main obstacle in my way. He had to be eliminated. I however, am in pocesion of one of the things he values in life.

The elevator stoped, and the doors slid open. "Sublevel D, sir," Delia said. I step out of the contraption and found myself in a very dark room. On the far side of the room stood chained a woman with orange hair tied into two short ponytails, blue round eyes, a small wedding dress with tears and burnt marks all throughout, her feet were bare and had symptoms of frostbite, and a necklace around her neck with a crescent moon charm on it.. The chains that held her up passed, through a mounted loop on the wall and ended at the collars of two Luxrays. Her eyes widened as I slowly approached her.

"W-what do you want?" She asked fearfully.

I stopped in front of her, my brown eyes gazing into hers, and asked, "I want you to tell me where Wes is?"

Her brows furrowed." I will not. How many times have I told you this before?"

"Wrong answer. "I snapped my fingers and the woman screamed as the Pokémon shocked her. After a few seconds, I sapped my fingers ceasing the torture. "I do not understand you. You know you would be scotch free had you told me about Wes' location. Yet, time after time you refuse to answer. Am I not being reasonable?" I asked.

"Heh. Reasonable, has does kidnapping someone and torturing them seem reasonable?" Rui asked. I snapped my fingers and her screams commenced. I let the pain last a little longer, so that it could sink in., before it once more ceased.

"You really do test my patience. If I cannot get information through you by normal means, then I have other methods that could make you talk," I stated. I could feel my lips curl into a smirk as Rui's eyes widened in horror. "But I am above such methods." I said, as I turned and made my way back to the elevator. Before entering however, I turned to face Rui one last time before saying," Oh and enjoy your stay."

"Wait." I stopped in my tracks. "Why are you doing this? I thought you were a good person." Rui asked me. I paused. She had asked me before and I had never given an answer. Maybe this time would be different.

"I plan to change this world. To better it. To make a world where someone else isn't harmed by someone else's selfish actions." I said, and with that I entered the elevator and made my way back to my office.

Once I arrived, and the Bookshelf closed behind me, I was once more greeted by Delilah.

"Sir. The Pokémon league champion is here for your meeting." The A.I stated.

"Thank you Delilah, please send her in," I commanded, as I made my way towards my desk, and taking a seat. A few moments later, the doors to my office opened to reveal a tall woman with blonde hair wearing a black cape that connected at her breasts, black jeans, a black shirt, and black heels.

I stood up from my seat. "Ah Cynthia. A pleasure to meet you."

"The pleasure is mine, Pathos. I heard that the Orre region wanted to be part of the league, and I had to come by to check it out," the blonde greeted with a smile.

"So you have been here before?" I asked, already knowing the answer.

"Yes indeed. I travelled her shortly after becoming the league champion. It was run down, and stricken with violence. I wanted to help, but there wasn't anything I could do," she paused, "But here I am, again. Not looking at a wasteland, but instead a flourishing region. Better yet the people wish to join the league."

"Yes. We have worked very hard to come where we are today. And yes we are hoping to join the league," I replied.

"Very well then. We will just need to appoint a champion and his elites, and it will all be settled, if you have already appointed gym leaders," Cynthia stated.

"Already done, I quickly stated.

Cynthia's eyes widened in shock. "How can that be only the league can select the champion and their elites?"

"We have already done so. It was…unanimous." I replied

"Ok then, who is the champion?" she asked.

"You're looking at him." I responded.

Cynthia's brows furrowed into a glare. "Oh really. If the people of orre region wants you as champion. You wouldn't mind having a battle with me, to prove so.

"You are weary. That is understandable. A person in a seat of power should not be involved with the league." I paused. "That is why I will agree to your battle. This Friday the Orre region will began hosting the world's largest tournament, in honor of our prosperity. We should open it off with our battle."

"That sounds reasonable, Pathos," Cynthia smiled. "I think league will have no problem selecting you as the regional champion." With that Cynthia made her way out of the office, only to stop at the threshold ad say ",I do hope that we could keep in contact Pathos" With her words finished, she made her way out of the building.

I turned back towards my office windows and stared out at the beautiful landscape. I took a few moments to take it in before saying, "Delia, contact the gym leaders and the elite four. We have five days to prepare, and we cannot waste any time."

"Will do, sir." The A.I stated.

"The perfect world is in near my grasps. I just need to reach out and grasp it," I said before turning around and making my way out of the building.


	2. Chapter 2

As I flew towards Karpedium City Gym, I thought about which Pokémon I would use to defeat Cynthia with, that coming Friday. I was stuck on using Charizard, for power sakes, or Garchomp, for showing her how outclass hers is. Charizard could create an intimidation factor, but so could Garchomp. Charizard could fly, while Garchomp could swim through the ground. Okay so he could not, but he could use dig, fast enough to be considered swimming in it.

I dismissed the conversation I was having with myself in favor of the current task at hand. Meeting the Karpedium city gym leader, Lilly. One of the most talented water type users I had ever seen in my life. Her Gyarados was simply a monster. Karpedium City, was rather small for a city and sat on the coast, and sat a two weeks journey away from Sunshore port. It beauty however comes from its aquarium. It doubles as both a tourist destination and the gym. However the only Pokémon that resides within it is the titan, Kyogre.

Within minutes Karpedium came within view. Its large buildings shinning in the sunlight. I continued my way to the southern coast where a large Dome like structure stood. This was the Karpedium city gym, a large cylinder building that was eighty meters in diameter, stood forty meters tall, and was toped of with an eighty meter half sphere. It stood at the waters edges overlapping the sea. I flew towards the front entrance of the building and withdrew my Charizard, before entering.

The gym was breathtaking, several rows of stands surrounded the water arena. Its design was very similar to the cerulean city gym. However unlike the Kanto region's water gym land Pokémon could stand on rock formation instead of floating blocks that could be easily knocked over.

"So the champion has finally come to visit me," A feminine voice called out to me. I looked down from the stands to find Lilly standing in the trainer's box on the far end of the arena. She was young, barely above the age of fifteen. She had short blue hair that dropped to her shoulders. She wore matching blue tank top and skin tight jeans that barely covered her blue sandals. All in all, you could easily tell she liked the color blue.

"Yes, I have. The tournament is this coming Friday, and I need to make sure everything is perfect," I responded as I jumped from the stands landing on the floor below.

"Alright then. Like old times sake you will battle each of the gym leaders. Like you did when you trained all of us." Lilly smiled.

"Yes as such. I will battle you, and just like before I will not hold back," I said as I threw out a pokeball. "Go, Charizard!" I shouted. The Pokeball opened and a white light shot out from it to reveal are large dragon like creature. It roared in furry as its eyes turned beat red.

The girl smirked. "Your Charizard is still menacing as ever. Go, Staryu." Lilly threw the pokeball and from it cane a large star fish with a giant red pearl in the middle.

I raised my eyebrow, not that she could see that or anything. "Tell me again; why you never evolved your Staryu into a Starmie?"

Lilly smiled. "Because Pathos. While Starmie is superior stats wise to Staryu. Starmie seconds as a psychic attack making it weak against dark, bug and ghost types."

I frowned. "Didn't I teach you that the best trainers find a way to overcome their Pokémon's vulnerabilities?"

Lilly sighed, "Yes I know, but aren't we in the middle of a battle."

"Yes. Yes we are," I replied. Silence was all you could hear. It was so deafening, you could hear a pin drop from a mile away. Silence remained, till all hell broke loose.

"Staryu use Hydro Pump!" Lilly shouted. A large burst of water shout out from the tip of Staryu's head, or whatever the hell you call it.

"Charizard Dodge and use Solar Beam." I commanded. Charizard roared as he flew into the air, before lifting his head up gathering a large green ball at the edge of his mouth.

"Staryu jump into the water!" Lilly shouted. Staryu jumped into the air just as a large beam of light crashed into land mass beneath it, creating a large cloud of dirt. When the cloud dissipated, Staryu was nowhere to be seen.

"Keep your eyes peeled, Charizard!" I shouted. The fire pokémon roared in agreement. Few sounds passed before I noticed a shadow in the water.

"Staryu use Rapid Spin, "Lilly commanded. Staryu immediately launched itself out of the water, spinning clock wise. Smashing into the fire pokémon's back. Knocking him back, but not out of the skies. "Staryu, keep using rapid spin," Lilly commanded with a smile.

Charizard roared in frustration as the starfish pokémon continued to hit him. I too growled in frustration. Staryu was a very annoying pokémon. On land it had an average speed, but in water its speed nearly doubles.

"Charizard use Thunder Punch when its midair." I commanded. Charizard roared in agreement.

Shortly after Staryu shot out of the water only to smash into Charizard electricity enhanced fist. Electricity coursed through the water pokémon's body as it crashed into another rock formation

"Get up, Staryu!" Lilly shouted. The star fish pokémon tried, but with no anvil.

"Now Charizard use Solar Beam," Once more a beam of light shot out of Charizard mouth this time colliding with the vulnerable pokémon. Charizard continued to fire the heavy stream of light, till I called it off with a wave of my hand. On the other side of the arena on disfigured rock formation lied Lilly's Staryu, its red gym blinking over and over.

"No, Staryu," the water trainer cried. She closes her eyes. Before pulling out a pokeball, and withdrew the fainted pokémon. Lilly opened her eyes and furrowed her brows at me

"What? I told you I wasn't holding back." I responded

Lilly Pulls out another pokeball. "I Know." She threw the said pokeball, and a white light shot out of it to reveal a giant blue dragon like creature. "Gyarados, Let's go!" the girl shouted. Gyarados roared in agreement.

Charizard roared in challenge. The two pokémon glared at one another. You could see the hatred in their eyes. The hatred of two pokémon always brought out a good match.

"Charizard use Solar Beam!" I shouted. A beam of light shot out of Charizard mouth, heading straight towards Lilly's gyaradoes.

"Gyaradoes, Hyper Beam!" The Gym leader shouted. An even larger beam of red and yellows shot out of Gyarados' mouth hurtling towards Charizard, The Hyper Beam ripped through the lesser Solar Beam, and Charizard was barely able to dodge the coming attack.

"Now. Gyaradoes, dive into the water." Gyarados roared in agreement before plunging itself deep into the blue liquid.

"Stay on your toes, Charizard," I commanded, as I searched for any signs of the water pokémon. By the time I saw its shadow it was too late.

"Gyarados, use Aqua Tail." The water pokémon's translucent tail shot out of the water and smacked Charizard to the other side of the arena.

"Dammit! Charizard get up!" I shouted. Charizard struggled, but did managed to get up.

Lilly pointed her index finger at Charizard. "Gyarados, Hyper beam!"

"Charizard, fly around it then use Thunder Punch!" Charizard roared in agreement, before flying towards gyaradoes flying around the red and yellow a circular manner. Charizard was merely a merger away from gyaradoes when it reeled back its right arm. Electricity crackled throughout his fist, as he smashed it into the water pokémon's face.

Gyarados cried out as the pokémon was knocked back into the water. Water splashed everywhere getting me and lily wet. Lilly glared ate me. "You bastard. You got me wet!" She shouted.

I raised my eyebrow at her. "Aren't you a water pokémon trainer?"

The water trainer continued to glare at me. "That is beside the point. If I wanted to get wet, I would have worn a swimsuit, or something!"

"I still don't see your point." I responded.

Lilly growled at me. "Damn you! Gyarados use Hyper Beam!" Lilly shouted.

"Charizard use Overheat!" I shouted. The fire pokémon began to glow red before a giant plume of fire shot out of charizard's mouth. The two forces collided one trying to overpower the other. Charizard glared at Gyarados, as Gyarados glared at Charizard. Sweat dripped down their faces as they continued to channel as much energy into their respective attacks. Charizard's Overheat began to falter against the Hyper Beam only for it to overpower the hyper beam when gyaradoes ceased its attack. The water pokémon cried out in pain as the large plume of fire engulfed it.

"Gyarados!" Lilly cried out, but the water pokémon was down for the count. Lilly pulled out a pokeball and withdrew her fainted Gyarados. Lilly put the said pokeball away before pulling out another pokeball. This one however, had a small water droplet on it.

I raised an eyebrow at her. "So you are going to use him. Aren't you?"

Lilly smiles. "The situation demands it." She then threw the pokémon ball. From it came a blue creature with a massive under bite and red spines on its back. The pokémon glared at Charizard before roaring in challenge. Charizard then roared in response. Forget what I said about her Gyarados, if I had known she would be using her Feraligatr, I would had called it a monster.

"Feraligatr, jump in the water." Lilly commanded. Firelighter roared before doing as such. This sent off red flags everywhere for me.

"Charizard! Fly up higher!" Charizard did, as such, just before feraligater shot out of the water, inteding to take a snap at his foot.

"Dammit almost had him. Feraligater, use Hydro pump!" Lilly shouted. A large jetstream of water shot out of feraligaters mouth.

"Charizard, dodge and use solarbeam!" Charizard did as such , before firing a large beam of light at shot out at feraligater.

"Feraligatr, dive back into the water." Firelighter body submerged ask into the water. Then the solar beam shot into the water causing the liquid to splash everywhere. Lilly once again became frustrated about being wet. "You Fucker! I swear to god, I am going to tear you a new asshole!" she shouted.

"Wow…What a dirty mouth you have. I wonder...if you have been doing other things then just pokémon battles." I smirked or at least tried to smirk.

"You god damn perv! Feraligatr now!" Lilly shouted. Just as I feared Feraligater launched itself out of the water, clamping its mouth on charizard's wing.

"Dammit. Charizard, use solar beam one last time." Charizard charged up a solar beam, then both Feraligatr and Charizard collided with the earth, sending up a cloud of dust. A bright light filled up the arena as feraligatr shot out of the dust cloud and into the arena walls. When the dust cloud disappeared Charizard could be seen standing roaring in triumph.

"It's not over yet Charizard!" I called out to Charizard. Charizard looked to me then glared at the wall where feraligatr had crashed into.

"Damn, right. It's not! Get, up Feraligatr!" Lilly shouted. The dust cloud dispersed and Feraligater glared at Charizard, as Charizard glared back. Both pokémon roared once more, and charged at one another.

"Feraligatr. Agua Tail!" Feraligater swung its translucent tail at Charizard.

"Charizard. Thunder punch!" Charizard threw an electrically enhanced fist at the Feraligatr.

Both moves collided causing Feraligatr to cry out in pain as electricity coursed through its body. With a loud thud Feraligatr fell to the ground unconscious.

"Dammit." Lilly spoke, as she withdrew her pokémon.

Charizard roared in triumph, before me to withdraw him. "Now that that's settled," I said before putting Charizard pokeball away and approached lily... "Can you tell me why you lost?"

Lilly sighed. "You baited me, and I fell for it. As a result I lost my temper."

"That is correct. A pokémon trainer must always keep his mind on the battle at hand. Otherwise they can make a mistake that could cost them." I responded.

"Mistakes that I had made." Lilly replied, her eyes glued to the floor.

"Lilly," I called out to her, the water trainer looked back up at me, her eyes watery. I rested a hand on her shoulder, trying to calm her nerves. "Yes. You did make a mistake, but you have grown so much since I first saw you."

Lilly's mood brightened as her eyes shined with joy, "Thank you, Pathos."

With a smile adorned my face. I turned and headed towards the entrance of the aquarium. "Way. You're all wet. Shouldn't you wash the salt out of your clothing first?" Lilly asked.

"The wind will dry me off," I stated as I made my way up a flight of stairs. "Oh and while at it. In case you run into any trouble here during the tournament. I will leave Kyogre here." I said before exiting the building and into the light of mid-day.

**Authors note:**

** Alright guys so sorry if it took me so long to type the story. I just had conflicting plans on what I had wanted to do for this story. Alright so we are having a poll for which pokémon our hero has on hand. We already know that he has Charizard and Garchomp, but there are many more he could have, so I am letting you decide.(And if not I already have a team selected. Just in case)**

**Venusaur**

**Blastoise**

**Kingler**

**Muk**

**Touros**

**Snorlax**

**Heracross**

**Meganium **

**Feraligatr**

**Typhlosion **

**Noctowl**

**Tyranitar **

**Donphan**

**Swellow**

**Torkoal**

**Crawdaunt **

**Sceptile**

**Glalie**

**Starraptor**

**Torterra**

**Monferno**

**Gliscor**

**Floatzel**

**Unfezant**

**Samurott**

**Seperior**

**Emboar**

**Leavanny**

**Seismitoad**

**Gigalith**

**Krookodile**

**Scrafty**

**Greninja**

**Talonflame**

**Noiverna **

**Hawlucha**

**Primeape**

**And if you do not like these you can always pick your own.**


End file.
